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Intercellular communication is quintessential for multicellularity and often mediated by secreted peptide ligands. In Metazoa, proprotein convertases are a major class of endoproteases partaking in the proteolytic processing of these ligands, which is in turn required for their signaling activities. In vertebrates, the best-studied convertase substrates are neuropeptides, peptide hormones, and members of the TGFβ/BMP-family. Each ligand is processed by a particular subset of convertases. Therefore, the diversification of convertases may have contributed to the growing complexity of cellular communication in metazoan evolution. However, proprotein convertases have not been systematically explored in Metazoa. Here, we sampled the representative metazoan genomes and established that six Kexin-like proprotein convertases were present in the last common ancestor of protostomes and deuterostomes. Among these, we identified a novel PCSKX orthologous group (OG) that was lost in vertebrates. Spiralian protosomes have, in general, maintained all six OGs. Therefore, we characterized the functional divergence of the Kexin-like OGs in the leechHelobdella, an experimentally tractable spiralian. Gene expression patterns suggested that PCSK1 and PCSK2 are specialized for the processing of neuropeptides and peptide hormones in bilaterians and that the newly identified PCSKX is probably functionally similar to furin and PCSK7. Finally, we showed that, distinct from the BMP morphogen in vertebrate embryos, the convertase-mediated proteolytic cleavage is not required for the short-range BMP signaling in the dorsoventral patterning of leech ectoderm. Together, our data revealed the complexity of the Kexin-like proprotein convertase gene family and their roles in generating diverse patterns of cellular communication in Metazoa.